Input data requirements

In greatR: Gene Registration from Expression and Time-Courses in R

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

The input data required for greatR is a data frame that contains gene expression time-course data with all replicates. The illustrated diagram below shows the required structure of the input.

knitr::include_graphics("figures/all_data_illustration_new.png")

This data frame must contain reference and query expression data which users wish to compare, and the following five columns:

• gene_id: locus name or unique ID of each gene.
• accession: accession or name of the reference and query data to compare.
• timepoint: time points of the gene expression data.
• expression_value: desired expression values or measure of the abundance of gene or transcripts which users wish to compare. This value can be RPM, RPKM, FPKM, TPM, TMM, DESeq, SCnorm, GeTMM, ComBat-Seq, and raw reads counts.
• replicate: biological replicate ID for an expression value at a particular time point.

Below we can see a real example of how the input data should look like:

# Load a data frame from the sample data
b_rapa_data <- system.file("extdata/brapa_arabidopsis_all_replicates.csv", package = "greatR") |>
  data.table::fread()

b_rapa_data[, .SD[1:2], by = accession][, .(gene_id, accession, timepoint, expression_value, replicate)] |>
  knitr::kable()

greatR documentation built on July 26, 2023, 5:43 p.m.